Do you mean that if enough content is placed in the right column or in the main content area, the footer stays fixed to the bottom of the screen and the content runs (over, under) below it?
This is quite common for fixed footer layouts when viewing them in DreamWeaver 'design' view, but isn't too common when viewed properly in a browser.
Naturally, if there is more content than there is screen space for, then something has to give. The normal behaviour for fixed footers is to sit at the bottom of the screen until the content pushes them down and the scrollbars begin. There are also 'truly' fixed footers that are designed to stay anchored to the bottom of the screen as you scroll down the content beyond screen height.
Could you post a link to an uploaded page where we can see this behaviour? It would be easier to diagnose the problem that way.